Biology subjects

Lynch, J. M.

Publications and source records attributed to Lynch, J. M..

2 recordsLinked to original sources

bioRxiv2025

RB-TnSeq elucidates dicarboxylic acid specific catabolism in β-proteobacteria for improved plastic monomer upcycling

Dicarboxylic acids are key components of many polymers and plastics, making them a target for both engineered microbial degradation and sustainable bioproduction. In this study, we generated a comprehensive dataset of functional evidence for the genetic basis of dicarboxylic and fatty acid metabolism using randomly-barcoded transposon sequencing (RB-TnSeq). We identified four {beta}-proteobacteria that displayed robust growth with dicarboxylic acid sole carbon sources and cultured their mutant libraries with dicarboxylic and fatty acids with carbon chain lengths from C3 to C12. The resulting fitness data suggested that dicarboxylic and fatty acid metabolisms are largely distinct, and different sets of {beta}-oxidation genes are required for catabolizing dicarboxylic versus fatty acids of the same carbon chain lengths. Additionally, we identified transcriptional regulators and transporters with strong fitness phenotypes related to dicarboxylic acid utilization. In Ralstonia sp. UNC404CL21Col (R. CL21), we deleted two transcriptional repressors to improve its utilization of short chain dicarboxylic acids. We exploited the diacid-utilizing catabolism of R. CL21 to upcycle a mock mixture of the dicarboxylic acids produced when polyethylene is oxidized. After introducing a heterologous indigoidine production pathway, this engineered Rastonia produced 0.56 {+/-} 0.02 g/L indigoidine from a mixture of dicarboxylic acids as a carbon source, demonstrating the potential of R. CL21 to upcycle plastics waste to products derived from tricarboxylic acid (TCA) cycle intermediates. ImportanceUpcycling the carbon in plastic wastes to value-added products is a promising approach to address the plastics waste and climate crises, and dicarboxylic acid metabolism is an important facet of several approaches. Improving our understanding of the genetic basis of this metabolism has the potential to uncover new enzymes and genetic parts for engineered pathways involving dicarboxylic acids. Our dataset is the most comprehensive interrogation of dicarboxylic acid catabolism to date, and this work will be of utility to researchers interested in both plastics bioproduction and upcycling applications.

microbiology↗

bioRxiv2024

Peatland restoration can provide climate change mitigation over all time-scales: A UK case-study

Peatlands provide one of the largest terrestrial carbon stocks in the UK. However, a large proportion of peatlands are drained for peat extraction, agriculture and other uses, turning them into a major source of the UKs land use greenhouse gas (GHG) emissions. Successful restoration can ultimately return peatlands into carbon sinks. However, rewetting - the primary step in peatland restoration - can reduce CO2 emissions while increasing CH4 emissions. This may result in little overall climate benefit, or even increased warming for several years post peatland restoration, as CH4 is a short-lived but strong GHG, and may overpower the reduction in CO2. Such consequences are rarely explored in detail, since most studies are based on comparing total CO2-equivalent emissions pre- and post-restoration using the 100-year Global Warming Potential (GWP100), which can fail to reveal the full dynamics. We evaluated the emissions and resultant climate impacts from peatland restoration using data from The Wildlife Trusts, a federation of UK-based conservation charities, as a case-study. The total emissions of each restoration stage were estimated by multiplying peatland areas under restoration with up-to-date UK emission factors (EF), then compared under multiple pulse emission metrics (GWP100, GWP20, GTP100) to indicate the impacts over a range of time-horizons, and GWP* to reveal the varying warming impacts over time. We also used Monte-Carlo Simulation to investigate the uncertainties in total emissions drawing from EF ranges. We found that the restoration so far has provided large emission reductions under all metrics, even considering the uncertainties. Increased CH4 is unlikely to cause extra warming in the extremely near-term (<20 years), and if the peatlands are maintained in their rewetted states, they can contribute to net-cooling in the long term. There is less certainty over the climate benefits of further restoration, from rewetted to "near-natural" states, especially in the shorter term, but we argue that any risks are low, while this continued restoration will provide further ecological benefits and support biodiversity. Our study lends further support for peatland restoration in the UK and other regions with similar habitats, and provides insight into the climate roles of peatlands more broadly.

ecology↗